RetrogeneDB ID:

retro_mmus_638

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:10:42330788..42331263(-)
Located in intron of:ENSMUSG00000038302
Retrocopy
information
Ensembl ID:ENSMUSG00000081873
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Snrpc
Ensembl ID:ENSMUSG00000024217
Aliases:Snrpc, Snrp1c, U1-C, U1C
Description:U1 small nuclear ribonucleoprotein C [Source:MGI Symbol;Acc:MGI:109489]


Retrocopy-Parental alignment summary:






>retro_mmus_638
ATGCCCAAGTTTTATTGTGACTACTGTGAAACTTATCTTACCCACGACTCTCCATCTGTGAGGAAGACACACTGCAGTGG
TTGGAAACCCAAAGAGAATGTGACAGACTATCACCAGAAAGGGATGGAAGATCAGGCCCAGAGCCTAATTGACAAGACAA
CGGCTGCATTTCAACAAGGGAAGATCCCTCCGCTCCGTTCTCTGCTCCTCCACCTGCAGGGGCCATGATTCCACTGCTCC
CCAGTCTCCTGAGTCCTCCTTGGCCTGGCATGATGCCTGCATCCCACATGGGAGACCCTCTCATGATGCCAGTGATGGGC
CCCCTCCTCCTGGGATGATGCCTGTGGGACCTGCTCCTGGGATGCAACCACCCATGGGAGGCCACATGCCCATGATGCCC
TGGCTTCCCATGATGAGACCTCCCGCCTGTCCTATGATGGTACCCACACAGCCTGGCATGACTCAGCCAGACAGA

ORF - retro_mmus_638 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.09 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMPKFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKIPP-APFSA
MPKFYCDYC.TYLTHDSPSVRKTHCSG.K.KENV.DY.QK.ME.QAQSLIDKTTAAFQQGKIPP.APFSA
RetrocopyMPKFYCDYCETYLTHDSPSVRKTHCSGWKPKENVTDYHQKGMEDQAQSLIDKTTAAFQQGKIPP<APFSA
ParentalPPPAGAMIPPPPSLPGPPRPGMMPAPHMGGPPMMPMM-GPPPPGMMPVGPAPGMRPPMGGHMPMMPGPPM
PPPAGAMIP..PSL..PP.PGMMPA.HMG.P.MMP.M.GPPPPGMMPVGPAPGM.PPMGGHMPMMP..PM
RetrocopyPPPAGAMIPLLPSLLSPPWPGMMPASHMGDPLMMPVM<GPPPPGMMPVGPAPGMQPPMGGHMPMMPWLPM
ParentalMRPPARPMMVPTRPGMTRPDR
MRPPA.PMMVPT.PGMT.PDR
RetrocopyMRPPACPMMVPTQPGMTQPDR

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain 0 .02 RPM 9 .32 RPM
SRP007412_cerebellum 0 .09 RPM 10 .86 RPM
SRP007412_heart 0 .09 RPM 7 .94 RPM
SRP007412_kidney 0 .06 RPM 11 .57 RPM
SRP007412_liver 0 .03 RPM 6 .69 RPM
SRP007412_testis 0 .00 RPM 51 .32 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_638 was not detected
No EST(s) were mapped for retro_mmus_638 retrocopy.
No TSS is located nearby retro_mmus_638 retrocopy 5' end.
retro_mmus_638 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_638 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 11 parental genes, and 91 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000012313 retrocopies
Callithrix jacchus ENSCJAG0000001532116 retrocopies
Monodelphis domestica ENSMODG000000139041 retrocopy
Mus musculus ENSMUSG00000024217 21 retrocopies
Nomascus leucogenys ENSNLEG000000083922 retrocopies
Oryctolagus cuniculus ENSOCUG000000266683 retrocopies
Otolemur garnettii ENSOGAG000000087559 retrocopies
Pongo abelii ENSPPYG000000172724 retrocopies
Rattus norvegicus ENSRNOG0000000049330 retrocopies
Sarcophilus harrisii ENSSHAG000000009451 retrocopy
Sus scrofa ENSSSCG000000015311 retrocopy



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